Approaching Dr. Borlaug’s Dream for High Nutrient Crops Through DNA Sequencing and Gene Editing for “Designer Crops”
Twenty years ago, in a hot yet greening corn field in Longli County, Guizhou Province of China, I was accompanying Dr. Norman Borlaug to visit a farmer’s field of QPM (Quality Protein Maize). I was then Vice President of the Chinese Academy of Agricultural Sciences (CAAS). I was involved in two of Dr. Borlaug’s trips to China during a few years’ time to promote QPM.
It is not a new idea of the 21st century to create “super crops.” Many agricultural pioneers envisioned crop varieties having simultaneously multiple superior traits, such as high yield, pest and disease resistance, high nutrition and adaptability to harsh environments. At the 2001 CGIAR Annual General Meeting, I listened to the keynote speech of World Food Prize Laureate Dr. Gurdev Khush, former Principal Plant Breeder of IRRI, entitled “Food Security by Design – Reinventing the Rice Plant in Partnership with NARES”. He traced IRRI’s endeavor of creating the “New Plant Type” of rice back to the last “Green Revolution.” Since the mid 1990s, IRRI has also led an international consortium on “redesigning rice photosynthesis,” aiming at transforming the rice plant from its “C3” photosynthesis mechanism into the “C4” photosynthesis that exists in such crops as maize, sugarcane and sorghum.
The attempt to design crops with a pyramid of ideal traits has been fueled in recent years by the CRISPR gene editing technology. The “CRISPR in China” series of the August 2, 2019, issue of Science magazine reviewed the progress the scientific community is making in advancing the CRISPR technology in not only China but the United States and other countries. According to the Science report, Chinese scientists in particular, championed by Drs. Gao Caixia and Li Jiayang of the Chinese Academy of Sciences, are becoming world leaders in achieving novel crop varieties with improved traits through CRISPR technology.
Notwithstanding the excitement and anxiety around the use and regulation of CRISPR, there is an urgent need to scale up the effort of mining the DNA information of the very basic material for gene editing--seeds, or crop germplasm. The Global Seed Vault in Svalbard, Norway, has around 6 million accessions of crop seeds. The CGIAR genebanks hold about 600,000, and China’s crop genebank at the Chinese Academy of Agricultural Sciences has 500,000 accessions. These genebanks, however, have only the basic information about the identity of the seeds collected, not their DNA sequences, or the “digital sequence information (DSI).” Value of the germplasm resources are their DNA information as much as the material itself. Systematically mining the germplasm collections, through DNA sequencing as well as genomic and phenotypic studies, will unlock the potential of the genetic materials and provide even more options for the world’s crop improvement effort.
Today’s DNA sequencing technologies have made it possible and affordable, which is not a trivial matter, to carry out large scale sequencing and resequencing of crop germplasm in a reasonably short time. While the first human genome project cost roughly $3 billion in 13 years, today it can be done in a day at a cost of a few hundred dollars.
The first rice genome was published in 2002. Last year, a team of scientists from IRRI, BGI (formerly known as the Beijing Genomics Institute) and the Chinese Academy of Agricultural Sciences published (Nature, 2018 April 25) their results of resequencing 3,000 accessions of rice with the discovery of 10,000 novel genes, among other findings. Recently, the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and BGI reported (Nature Genetics, 2019 April 29) the results of resequencing 429 accessions of chickpea, an important staple for millions in developing countries, that provides insights into its genome diversity, domestication and agronomic traits.
The China National Genebank (CNGB), Shenzhen, is a non-profit and unique science facility that integrates the functions of storing, DNA sequencing and gene synthesis for the genetic resources. It started functioning in 2016, and was built and owned by the Chinese government with BGI Research Institute and BGI College, which are both non-profit, as key partners. CNGB has the capacity to store 25 million biological samples at temperatures of 4oC to -196oC. The CNGB sequencing platform has perhaps the world’s largest capacity for genome sequencing, producing up to 20 PB (petabytes) of data per year. It can sequence 5,800 rice genomes in a day, at the same sequencing depth (20X) as the first rice genome sequenced in 2002.
The singularity is near. Technically speaking, Dr. Borlaug’s dream for a hunger-free world is within reach in the truly new era of crop improvement, and the new genomics science can contribute profoundly to achieving that goal.